Parallel detection of intrinsic fluorescence from peptides and proteins for quantification during mass spectrometric analysis

Protein classification by autofluorescence spectral shape analysis using machine learning

Depending on the relative numbers and spatial arrangement of Tryptophan (Trp; W) and Tyrosine (Tyr; Y) residues, different proteins produce distinct autofluorescence (AF) spectral shapes when excited at ∼280 nm. Yet, considering the vast number and heterogeneous forms in nature, visual analysis and precise identification of proteins based on their AF spectra is challenging and further compounded in cases when different proteins produce substantially similar AF spectral shapes. There is, thus, a serious need to develop a methodology to address this problem. The current study proposes a practical technology to quickly identify proteins using machine learning (ML) algorithms based on their AF spectra. Specifically, AF spectra of fifteen different standard proteins of varying origin with distinct structural and Trp/Tyr compositions were recorded; based on the spectral features selected by the Minimum-Redundancy-Maximum-Relevance (mRMR) algorithm, a multiclass Support Vector Machine (SVM) learning model with Radial Basis Function (RBF), Polynomial, and Linear kernels classified the proteins with high accuracy of 99.06%, 99.03%, and 98.29% respectively. Since protein identification is the key to understand biological functions and disease diagnosis, the proposed methodology could offer a viable alternative to and improve the existing protein identification techniques.

Discovery of Potential Antituberculosis Agents Targeted Methionine Aminopeptidase 1 of Mycobacterium tuberculosis by the Developed Fluorescent Probe

Tuberculosis (TB) is a chronic systemic infectious disease caused by Mycobacterium tuberculosis (M. tuberculosis). Methionine aminopeptidase 1 (MtMET-AP1) is a hydrolase that mediates the necessary post-translational N-terminal methionine excision (NME) of peptides during protein synthesis, which is necessary for bacterial proliferation and is a potential target for the treatment of tuberculosis. Based on the functional characteristics of MtMET-AP1, we developed an enzymatic activated near-infrared fluorescent probe DDAN-MT for rapid, highly selective, and real-time monitoring of endogenous MtMET-AP1 activity in M. tuberculosis. Using the probe DDAN-MT, a visually high-throughput screening technique was established, which obtained three potential inhibitors (GSK-J4 hydrochchloride, JX06, and lavendustin C) against MtMET-AP1 from a 2560 compounds library. More importantly, these inhibitors could inhibit the growth of M. tuberculosis H37Ra especially (MICs < 5 μM), with low toxicities on intestinal bacteria strains and human cells. Therefore, the visual sensing of MtMET-AP1 was successfully performed by DDAN-MT, and MtMET-AP1 inhibitors were discovered as potential antituberculosis agents.

A comprehensive review on LED-induced fluorescence in diagnostic pathology

Sensitivity, specificity, mobility, and affordability are important criteria to consider for developing diagnostic instruments in common use. Fluorescence spectroscopy has been demonstrating substantial potential in the clinical diagnosis of diseases and evaluating the underlying causes of pathogenesis. A higher degree of device integration with appropriate sensitivity and reasonable cost would further boost the value of the fluorescence techniques in clinical diagnosis and aid in the reduction of healthcare expenses, which is a key economic concern in emerging markets. Light-emitting diodes (LEDs), which are inexpensive and smaller are attractive alternatives to conventional excitation sources in fluorescence spectroscopy, are gaining a lot of momentum in the development of affordable, compact analytical instruments of clinical relevance. The commercial availability of a broad range of LED wavelengths (255-4600 nm) has opened up new avenues for targeting a wide range of clinically significant molecules (both endogenous and exogenous), thereby diagnosing a range of clinical illnesses. As a result, we have specifically examined the uses of LED-induced fluorescence (LED-IF) in preclinical and clinical evaluations of pathological conditions, considering the present advancements in the field.

Relationship among the minor constituents, antibacterial activity and geographical origin of honey: A multifactor perspective

Some minor constituents of honey samples were determined through a fluorometric-chemical characterization method and related multifactorially with their antibacterial activity against Staphylococcus aureus and Pseudomonas aeruginosa and with their geographical origin. Rotated principal component analysis identified five significant components in honey: three related to antibacterial activity and linked to phenolic compounds; Maillard products; proteins; the concentration of H₂O₂ at 3 and 24 h of incubation; and a tyrosine-containing entity. On the other hand, five constituents (phenolic compounds were the most relevant) allowed the classification of honey samples by geographical origin with 87% certainty. The results showed that phenolic compounds and Maillard products are related to the sustained production of H₂O₂ over time, which in turn boosts the antibacterial activity of honey. Native flora could promote this capability. The results showed the effect of geographic origin on the content of the analyzed minor constituents of honey, particularly phenolic compounds.

Improved Quantitation of Gluten in Wheat Starch for Celiac Disease Patients by Gel-Permeation High-Performance Liquid Chromatography with Fluorescence Detection (GP-HPLC-FLD)

Purified wheat starch (WSt) is commonly used in gluten-free products for celiac disease (CD) patients. It is mostly well-tolerated, but doubts about its safety for CD patients persist. One reason may be that most ELISA kits primarily recognize the alcohol-soluble gliadin fraction of gluten, but insufficiently target the alcohol-insoluble glutenin fraction. To address this problem, a new sensitive method based on the sequential extraction of gliadins, glutenins, and gluten from WSt followed by gel-permeation high-performance liquid chromatography with fluorescence detection (GP-HPLC-FLD) was developed. It revealed that considerable amounts of glutenins were present in most WSt. The gluten contents quantitated by GP-HPLC-FLD as sum of gliadins and glutenins were higher than those by R5 ELISA (gluten as gliadin content multiplied by a factor of 2) in 19 out of 26 WSt. Despite its limited selectivity, GP-HPLC-FLD may be applied as confirmatory method to ELISA to quantitate gluten in WSt.

Ultraviolet Photodissociation Induced by Light-Emitting Diodes in a Planar Ion Trap

The first application of light-emitting diodes (LEDs) for ultraviolet photodissociation (UVPD) mass spectrometry is reported. LEDs provide a compact, low cost light source and have been incorporated directly into the trapping cell of an Orbitrap mass spectrometer. MS/MS efficiencies of over 50 % were obtained using an extended irradiation period, and UVPD was optimized by modulating the ion trapping parameters to maximize the overlap between the ion cloud and the irradiation volume.

A fiber optic, ultraviolet light-emitting diode-based, two wavelength fluorometer for monitoring reactive adsorption

Construction and use of an ultraviolet light-emitting diode-based fluorometer for measuring photoluminescence (PL) from powder samples with a fiber optic probe is described. Fluorescence at two wavelengths is detected by miniature photomultiplier tubes, each equipped with a different band pass filter, whose outputs are analyzed by a microprocessor. Photoluminescent metal oxides and hydroxides, and other semiconducting nanoparticles, often undergo changes in their emission spectra upon exposure to reactive gases, and the ratio of the PL intensities at two wavelengths is diagnostic of adsorption. Use of this instrument for reactive gas sensing and gas filtration applications is illustrated by measuring changes in the PL ratio for zirconium hydroxide and zinc oxide particles upon exposure to air containing low concentrations of sulfur dioxide.

High-performance liquid chromatography combined with intrinsic fluorescence detection to analyse melittin in individual honeybee (Apis mellifera) venom sac

Melittin is the major toxin peptide in bee venom, which has diverse biological effects. In the present study, melittin was separated by reverse-phase high-performance liquid chromatography, and was then detected using intrinsic fluorescence signal of tryptophan residue. The accuracy, linearity, limit of quantitation (LOQ), intra-day and inter-day precision of the method were carefully validated in this study. Results indicate that the intrinsic fluorescence signal of melittin has linear range from 0.04μg/mL to 20μg/mL with LOQ of 0.04μg/mL. The recovery range of spiked samples is between 81.93% and 105.25%. The precision results are expressed as relative standard deviation (RSD), which is in the range of 2.1-7.4% for intra-day precision and 6.2-10.8% for inter-day precision. Because of the large linear dynamic range and the high sensitivity, intrinsic fluorescence detection (IFD) can be used for analyzing melittin contents in individual venom sac of honeybee (Apis mellifera). The detected contents of melittin in individual bee venom sac are 0.18±0.25μg for one-day old honeybees (n=30), and 114.98±43.51μg for 25-day old (n=30) honeybees, respectively. Results indicate that there is large bee-to-bee difference in melittin contents. The developed method can be useful for discovering the melittin related honeybee biology information, which might be covered in the complex samples.

Trimethylation enhancement using diazomethane (TrEnDi): rapid on-column quaternization of peptide amino groups via reaction with diazomethane significantly enhances sensitivity in mass spectrometry analyses via a fixed, permanent positive charge

Defining cellular processes relies heavily on elucidating the temporal dynamics of proteins. To this end, mass spectrometry (MS) is an extremely valuable tool; different MS-based quantitative proteomics strategies have emerged to map protein dynamics over the course of stimuli. Herein, we disclose our novel MS-based quantitative proteomics strategy with unique analytical characteristics. By passing ethereal diazomethane over peptides on strong cation exchange resin within a microfluidic device, peptides react to contain fixed, permanent positive charges. Modified peptides display improved ionization characteristics and dissociate via tandem mass spectrometry (MS(2)) to form strong a2 fragment ion peaks. Process optimization and determination of reactive functional groups enabled a priori prediction of MS(2) fragmentation patterns for modified peptides. The strategy was tested on digested bovine serum albumin (BSA) and successfully quantified a peptide that was not observable prior to modification. Our method ionizes peptides regardless of proton affinity, thus decreasing ion suppression and permitting predictable multiple reaction monitoring (MRM)-based quantitation with improved sensitivity.

Fast mass spectrometry detection of tryptophan-containing peptides and proteins by reduction with pyridine-borane

In this note, we describe a method devised to detect, by means of mass spectrometry (MS), tryptophan-containing peptides and proteins using pyridine-borane. This reagent selectively reduces tryptophan residues, converting them to 2,3-dihydro-tryptophan, thereby enabling quantitation of tryptophans.

Characterization and quantification of intact 26S proteasome proteins by real-time measurement of intrinsic fluorescence prior to top-down mass spectrometry

Quantification of gas-phase intact protein ions by mass spectrometry (MS) is impeded by highly-variable ionization, ion transmission, and ion detection efficiencies. Therefore, quantification of proteins using MS-associated techniques is almost exclusively done after proteolysis where peptides serve as proxies for estimating protein abundance. Advances in instrumentation, protein separations, and informatics have made large-scale sequencing of intact proteins using top-down proteomics accessible to the proteomics community; yet quantification of proteins using a top-down workflow has largely been unaddressed. Here we describe a label-free approach to determine the abundance of intact proteins separated by nanoflow liquid chromatography prior to MS analysis by using solution-phase measurements of ultraviolet light-induced intrinsic fluorescence (UV-IF). UV-IF is measured directly at the electrospray interface just prior to the capillary exit where proteins containing at least one tryptophan residue are readily detected. UV-IF quantification was demonstrated using commercially available protein standards and provided more accurate and precise protein quantification than MS ion current. We evaluated the parallel use of UV-IF and top-down tandem MS for quantification and identification of protein subunits and associated proteins from an affinity-purified 26S proteasome sample from Arabidopsis thaliana. We identified 26 unique proteins and quantified 13 tryptophan-containing species. Our analyses discovered previously unidentified N-terminal processing of the β6 (PBF1) and β7 (PBG1) subunit - such processing of PBG1 may generate a heretofore unknown additional protease active site upon cleavage. In addition, our approach permitted the unambiguous identification and quantification both isoforms of the proteasome-associated protein DSS1.